Ocean adapt exploration script

Ocean adapta data

By species data exploration

• for each region, year, species combination, the mean location and biomass, shows species averages.

By species data exploration

• for every region and year, all of the species for that region, including zeros if they were not present.

O.K. so now we have a wtcpue column here. Lets now get some data wrangling going and exploration figures

Survey plots

plot_data <- dat_exploded %>% 
  group_by(spp,year,lat,lon,depth) %>%
  summarise_if(is_numeric,mean,na.rm=T) %>%
  mutate(
    year = as.numeric(year)
  )

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Histogram of data points

Timeline of depth and wtcpue

Boxplot of data

Survey maps

us_map <- st_as_sf(map("state", plot = FALSE, fill = TRUE))

path_world <- MyFunctions::my_path("G", extra_path = "Spatial/SAU/SAU_Shapefile")
path_world <- "~/Downloads/SAU_Shapefile"

# The File
fnam_world <- "SAUEEZ_July2015.shp"

# Load it!
World_eez_sf <- st_read(dsn = path_world,
                        layer =file_path_sans_ext(fnam_world)) %>% 
  rename(eez_name = Name) %>% 
  st_transform(crs = 4326) %>% # 4326
  # st_transform(crs = "+proj=eck4") %>% # for tbular plot
  st_simplify(preserveTopology = TRUE, dTolerance = 0.1) %>% 
  filter(eez_name == "USA (East Coast)")

# Set manual breaks for bins
bins <- seq(1970,2020,5)

map_data <- dat_exploded %>% 
  group_by(spp,year,lat,lon,depth) %>%
  summarise_if(is_numeric,mean,na.rm=T) %>%
  mutate(
    year = as.numeric(year),
    period = cut(year, breaks = bins)
  ) %>% 
  group_by(period,lat,lon) %>% 
  summarise_if(is.numeric,mean,na.rm=T) %>% 
  filter(wtcpue>0) 

Map of smapling points

In this case the color gradiant represents year from 1972 to 2019

Density map

This is a simple 2d kenell analysis using ggplot2::stat_density_2d() of the sampling points

Looks to me that the stock might not be shifting per se but expanding its northern range

CPUE (wt CPUE) data

ggplot(us_map) +
  geom_sf() +
  geom_sf(data = World_eez_sf, aes(), fill = "white") +
  geom_point(data = subset(map_data, wtcpue < 100),
             aes(
               x = lon,
               y = lat,
               color = wtcpue
             ),
             
  ) +
  # facet_wrap(~period,
  #            nrow = 2) +
  scale_color_distiller(palette = "Spectral", 
                       guide_legend(title = "CPUE")) + 
  # viridis::scale_fill_viridis() +
  # viridis::scale_colour_viridis() +
  coord_sf(xlim = c(-76, -65),ylim = c(35, 45)) +
  MyFunctions::my_ggtheme_m()
)

Error: unexpected ')' in ")"

ERDDAP

This is the data extracted directly from NOAA in has four available surveys (OceanAdapt only two)

• Northeast Fisheries Science Center (NEFSC) Fall Bottom Trawl Survey
  

• Northeast Fisheries Science Center (NEFSC) Spring Bottom Trawl Survey

• Northeast Fisheries Science Center (NEFSC) Summer Bottom Trawl Survey

• Northeast Fisheries Science Center (NEFSC) Winter Bottom Trawl Survey

• Black seabass code is 141